Acetogenins Exhibit Potential BCL-XL Inhibitor for the Induction of Apoptosis in the Molecular Docking Study

2021 ◽  
Vol 18 ◽  
Author(s):  
Noraziah Nordin ◽  
Kaynat Khimani ◽  
Mohd Faiz Abd Ghani
Keyword(s):  
Molecular Docking ◽  
Cancer Chemotherapy ◽  
Chemotherapy Resistance ◽  
Docking Simulation ◽  
Docking Study ◽  
Biological Properties ◽  
Vital Role ◽  
Molecular Docking Study ◽  
Good Target ◽  
Induction Of Apoptosis

Background: Anti-apoptotic protein BCL-XL plays a vital role in tumorigenesis and cancer chemotherapy resistance, resulting in a good target for cancer treatment. Understanding the function of BCL-XL has driven the progression of a new class of cancer drugs that can mimic its natural inhibitors, BH3-only proteins to trigger apoptosis. This mimicking is initiated through acetogenins due to their excellent biological properties. Acetogenins which can be isolated from Annonaceae plants, have a unique structure along with several oxygenated functionalities. Objective: Based on their biological capability, various acetogenins were studied in the present study and compared alongside with ABT-737 on molecular docking. Methods: The docking simulation of acetogenins was performed using AutoDock Vina software. Results: Our findings have shown eleven acetogenins-BCL-XL protein complex, namely, muricin B (2), muricin F (4), muricin H (6), muricin I (7), xylomaticin (9), annomontacin (12), annonacin (14), squamocin (15), squamostatin A (16), bullatacin (20) and annoreticulin (21) exhibited strong binding affinities lower than – 10.4 kcalmol-1 as compared to ABT-373-BCL-XL complex. Six hydrogen bonds along with hydrophobic interaction were detected on the complex of BCL-XL with muricin B (2), muricin G (5), corossolone (11) and isoannonacin-10-one A (18). Conclusion: These findings indicated that some acetogenins could represent a new potential BCL-XL inhibitor which could mimic the BH3-only protein for the induction of apoptosis in cancer chemotherapy.

scholarly journals Design, Synthesis, and Molecular Docking Study of New Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Inhibitors Combining Resin Acids and Adamantane Moieties

2021 ◽  
Vol 14 (5) ◽  
pp. 422
Author(s):  
Kseniya Kovaleva ◽  
Olga Yarovaya ◽  
Konstantin Ponomarev ◽  
Sergey Cheresiz ◽  
Amirhossein Azimirad ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Biological Properties ◽  
Glioma Cell Line ◽  
Resin Acids ◽  
Adamantane Derivatives ◽  
Molecular Docking Study ◽  
Design Synthesis ◽  
Low Cytotoxicity ◽  
Covalent Intermediate

In this paper, a series of novel abietyl and dehydroabietyl ureas, thioureas, amides, and thioamides bearing adamantane moieties were designed, synthesized, and evaluated for their inhibitory activities against tyrosil-DNA-phosphodiesterase 1 (TDP1). The synthesized compounds were able to inhibit TDP1 at micromolar concentrations (0.19–2.3 µM) and demonstrated low cytotoxicity in the T98G glioma cell line. The effect of the terpene fragment, the linker structure, and the adamantane residue on the biological properties of the new compounds was investigated. Based on molecular docking results, we suppose that adamantane derivatives of resin acids bind to the TDP1 covalent intermediate, forming a hydrogen bond with Ser463 and hydrophobic contacts with the Phe259 and Trp590 residues and the oligonucleotide fragment of the substrate.

An insight on safety, efficacy, and molecular docking study reports of N-acetylcysteine and its compound formulations

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Laiba Rind ◽  
Mohammad Ahmad ◽  
Mohammad Irfan Khan ◽  
Badruddeen ◽  
Juber Akhtar ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Analytical Techniques ◽  
Docking Study ◽  
Biological Properties ◽  
Docking Studies ◽  
Pharmaceutical Product ◽  
Fixed Dose ◽  
Molecular Docking Study

Abstract N-acetylcysteine (NAC) is considered as the body’s major antioxidant molecules with diverse biological properties. In this review, the pharmacokinetics, safety and efficacy report on both the preclinical and clinical summary of NAC is discussed. Both in vitro and in vivo preclinical studies along with the clinical data have shown that NAC has enormous biological properties. NAC is used in the treatment of acetaminophen poisoning, diabetic nephropathy, Alzheimer’s disease, schizophrenia, and ulcerative colitis, etc. Numerous analytical techniques, for instance, UPLC, LC-MS, HPLC, RP-IPC are primarily employed for the estimation of NAC in different single and fixed-dose combinations. The molecular docking studies on NAC demonstrate the binding within Sudlow’s site-I hydrogen bonds and formation of NAC and BSA complexes. Various hydrophobic and hydrophilic amino acids generally exist in making contact with NAC as NAC-BSA complexes. Docking studies of NAC with the active site of the urease exposed an O-coordinated bond through nickel 3002 and a hydrogen bond through His-138. NAC and its analogs also made the allosteric pockets that helped to describe almost all favorable pose for the chaperone in a complex through the protein. Thus, we intended to highlight the several health benefits of this antioxidant compound and applications in pharmaceutical product development.

scholarly journals Synthesis, Antimicrobial Study, and Molecular Docking Simulation of 3,4-Dimethoxy-β-Nitrostyrene Derivatives as Candidate PTP1B Inhibitor

2020 ◽  
Vol 88 (3) ◽  
pp. 37
Author(s):  
Salman Alfarisi ◽  
Mardi Santoso ◽  
Alfinda Novi Kristanti ◽  
Imam Siswanto ◽  
Ni Nyoman Tri Puspaningsih
Keyword(s):  
Molecular Docking ◽  
Signaling Pathways ◽  
Metabolic Diseases ◽  
Tyrosine Phosphatase ◽  
Docking Simulation ◽  
Docking Study ◽  
Negative Regulator ◽  
Potential Candidate ◽  
Molecular Docking Study ◽  
Cell Functions

A derivative series of 3,4-dimethoxy-β-nitrostyrene was synthesized through nitroaldol reaction, including a new compound of 3,4-ethylenedioxy-β-bromo-β-nitrostyrene. The antimicrobial activity effect of 3,4-alkyloxy modification of β-nitrostyrene was investigated. A molecular docking study was also performed to obtain information about their interactions with protein tyrosine phosphatase 1B (PTP1B). The active residues of cysteine-215 and arginine-221 of PTP1B play a key role in signaling pathways that regulate various microorganism cell functions. It also acts as a negative regulator in signaling pathways of insulin that are involved in type 2 diabetes and other metabolic diseases. These derivatives exhibited potential antifungal activity. The studied compounds were also had potential as fragments to be PTP1B inhibitors by interacting with serine-216 and arginine-221 residues, according to their molecular docking. 3,4-Ethylenedioxy-β-methyl-β-nitrostyrene was the most successful potential candidate as a PTP1B inhibitor. However, further research is needed to investigate their potential for medicinal use.

scholarly journals A New N-Substituted 1H-Isoindole-1,3(2H)-Dione Derivative—Synthesis, Structure and Affinity for Cyclooxygenase Based on In Vitro Studies and Molecular Docking

2021 ◽  
Vol 22 (14) ◽  
pp. 7678
Author(s):  
Dominika Szkatuła ◽  
Edward Krzyżak ◽  
Paulina Stanowska ◽  
Magdalena Duda ◽  
Benita Wiatrak
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Biological Properties ◽  
Molecular Ions ◽  
Molecular Docking Study ◽  
Lipinski’S Rule ◽  
Cox 2 ◽  
Probable Path ◽  
Cox 1

Isoindoline-1,3-dione derivatives constitute an important group of medicinal substances. In this study, nine new 1H-isoindole-1,3(2H)-dione derivatives and five potential pharmacophores were obtained in good yield (47.24–92.91%). The structure of the new imides was confirmed by the methods of elemental and spectral analysis: FT–IR, H NMR, and MS. Based on the obtained results of ESI–MS the probable path of the molecules decay and the hypothetical structure of the resulting pseudo-molecular ions have been proposed. The physicochemical properties of the new phthalimides were determined on the basis of Lipiński’s rule. The biological properties were determined in terms of their cyclooxygenase (COX) inhibitory activity. Three compounds showed greater inhibition of COX-2, three compounds inhibited COX-1 more strongly than the reference compound meloxicam. From the obtained results, the affinity ratio COX-2/COX-1 was calculated. Two compounds had a value greater than that of meloxicam. All tested compounds showed oxidative or nitrosan stress (ROS and RNS) scavenging activity. The degree of chromatin relaxation outside the cell nucleus was lower than the control after incubation with all test compounds. The newly synthesized phthalimide derivatives showed no cytotoxic activity in the concentration range studied (10–90 µM). A molecular docking study was used to determined interactions inside the active site of cyclooxygenases.

scholarly journals Hit Identification of a Novel Quinazoline Sulfonamide as a Promising EphB3 Inhibitor: Design, Virtual Combinatorial Library, Synthesis, Biological Evaluation, and Docking Simulation Studies

2021 ◽  
Vol 14 (12) ◽  
pp. 1247
Author(s):  
Kyeong Lee ◽  
Hossam Nada ◽  
Hyun Jung Byun ◽  
Chang Hoon Lee ◽  
Ahmed Elkamhawy
Keyword(s):  
Molecular Docking ◽  
Combinatorial Library ◽  
Binding Free Energy ◽  
Biological Activities ◽  
Hybrid Approach ◽  
Docking Simulation ◽  
Docking Study ◽  
Biological Evaluation ◽  
Molecular Docking Study ◽  
Hit Identification

EphB3 is a major key player in a variety of cellular activities, including cell migration, proliferation, and apoptosis. However, the exact role of EphB3 in cancer remains ambiguous. Accordingly, new EphB3 inhibitors can increase the understanding of the exact roles of the receptor and may act as promising therapeutic candidates. Herein, a hybrid approach of structure-based design and virtual combinatorial library generated 34 quinazoline sulfonamides as potential selective EphB3 inhibitors. A molecular docking study over EphB3 predicted the binding affinities of the generated library, and the top seven hit compounds (3a and 4a–f), with GlideScore ≥ −6.20 Kcal/mol, were chosen for further MM-GBSA calculations. Out of the seven top hits, compound 4c showed the highest MM-GBSA binding free energy (−74.13 Kcal/mol). To validate these predicted results, compounds 3a and 4a–f were synthesized and characterized using NMR, HRMS, and HPLC. The biological evaluation revealed compound 4c as a potent EphB3 inhibitory lead (IC50 = 1.04 µM). The screening of 4c over a mini-panel of kinases consisting of EGFR, Aurora A, Aurora B, CDK2/cyclin A, EphB1, EphB2, EphB4, ERBB2/HER2, and KDR/VEGFR2, showed a promising selective profile against EphB3 isoform. A dose-dependent assay of compound 4c and a molecular docking study over the different forms of EphB provided insights into the elicited biological activities and highlighted reasonable explanations of the selectivity.

scholarly journals GLYCOGEN SYNTHASE KINASE-3 BETA PROTEIN INHIBITION BY SELECTED PHYTOCOMPOUNDS IN SILICO

2016 ◽  
Vol 10 (1) ◽  
pp. 87
Author(s):  
Vanitha Varadharaj ◽  
Naresh Kandakatl
Keyword(s):  
Molecular Docking ◽  
Glycogen Synthase ◽  
Protein A ◽  
Experimental Studies ◽  
Docking Simulation ◽  
Docking Study ◽  
Glycogen Synthase Kinase ◽  
Glycogen Synthase Kinase 3 ◽  
Molecular Docking Study ◽  
Gsk 3Β

ABSTRACTObjectives: Bioactive phytocompounds are a rich source of chemopreventive substance. In the present investigation, docking study was performedfor the selected bioactive phytocompounds such as oleanolic acid, ecdysterone, betaine, stigmasterol acetate, and cinnamic acid to evaluate theiraffinity to glycogen synthase kinase-3 beta (GSK-3β) protein, a wound-healing biomarker. 2-chloro-5-[4-(3-chloro-phenyl)-2, 5-dioxo-2,5-dihydro-1hpyrrol-3-ylamino]-benzoicacid wasused as an inhibitorforGSK-3βwith minimum binding energy(−31.5 kcal/mol).Methods: Molecular docking study was conducted using AutoDock 4.2 version and the visualization result using Discover Studio 4.5.Results: The docking analysis ranked the selected phytocompounds that have high theoretical scores to bind to the proteins. The binding mode of thephytocompounds that bound to all the target proteins with high affinity was studied. The simulation demonstrated that the protein-ligand complexstabilized by multiple hydrogen bonds (H-bonds) was preferentially formed at the catalytic site. The results highlighted in this study reveals thatamong the selected lead phytocompounds that docked into the active site of GSK-3β, ecdysterone showed acceptable 6 H-bond interactions withresidues LYS85, TYR134, ARG141, GLN185, ASP200, PRO136 when compared to the reference compound with 5 H-bond interactions.Conclusion: Thus, based on the docking score ecdysterone could be considered as a novel compounds that can be used for experimental studies forthe inhibition of GSK-3β kinase. These results can be helpful for further design of novel GSK-3β inhibitors.Keywords: Phytocompounds, Molecular docking, Simulation, Receptor, Ligand, Inhibition.

scholarly journals Ethanolic Extract of Hedyotis corymbosa and Its Combination with 5-FU Inhibit Cyclin D Expression on WiDr Colorectal Cancer Cell

2017 ◽  
Vol 7 (1) ◽  
pp. 25 ◽  
Author(s):  
Argandita Meiftasari ◽  
Januar Caesar W.P. ◽  
Annisa Novarina ◽  
Julika Yovi W. ◽  
Riris Istighfari Jenie
Keyword(s):  
Colorectal Cancer ◽  
Molecular Docking ◽  
Ursolic Acid ◽  
Cancer Cell ◽  
Docking Simulation ◽  
Ethanolic Extract ◽  
Docking Study ◽  
Antiproliferative Effect ◽  
Cyclin D ◽  
Molecular Docking Study

Hedyotis corymbosa has been used for long time as an important component in several folklore medicine formula to clinically treat various types of cancer, including colorectal cancer (CRC). Previously, Hedyotis corymbosa ethanolic extract (HEE) which contain ursolic acid reported to inhibit CRC growth via induction of cancer cell apop­tosis and blocked the cell cycle, preventing G1 to S progression where cyclin D highly espressed in this phase. 5-fluorouracil (5FU), the first line chemotherapy of colorectal cancer have had resistence and possessed several side effects such as neutropenia, immunosuppression, diarrhea, and also constipation. Therefore, the aim of this research is to conduct the antiproliferative effect and molecular analysis of HEE and its combination with 5FU. Molecular docking study was also done to approach the specific protein target of the compound. Antiproliferative effect was conducted by MTT assay, while cyclin D expression  was examined by immunofluorescence. The proliferative effect showed that both HEE and 5-FU had cytotoxic effect with IC50 value of 65 µg/mL and 90 µM respectively, meanwhile the combination of HEE and 5FU have synergism effect with CI = 0.48 on dose HEE = 22 µg/mL and 5FU= 6.25 µM. Immunofluorescence assay showed HEE and its combination with 5FU suppressed the expression of cyclin D. From molecular docking simulation, ursolic acid performed stable interaction with cyclin D. Our findings suggest that HEE may be an effective treat­ment for co-chemotherapic for 5-FU through inhibition of cyclin D expression.Keywords : Hedyotis corymbosa, 5-fluorouracil, colorectal cancer,  WiDr, cyclin D 

EVALUATION OF IN-SILICO ANTICANCER POTENTIAL OF PYRETHROIDS: A COMPARATIVE MOLECULAR DOCKING STUDY

2015 ◽  
Author(s):  
Manik Ghosh ◽  
Kamal Kant ◽  
Anoop Kumar ◽  
Padma Behera ◽  
Naresh Rangra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Study ◽  
Molecular Docking Study

Myricetin Preferentially Binds to Interfacial Regions in Domains 1 – 3 to Inhibit Cholesterol-Dependent Cytolysins: A Molecular Docking Study

2020 ◽  
Author(s):  
Rafael Espiritu
Keyword(s):  
Molecular Docking ◽  
Structural Changes ◽  
Docking Study ◽  
Listeriolysin O ◽  
Molecular Docking Study ◽  
Docking Analysis ◽  
Streptolysin O ◽  
Molecule Inhibitor ◽  
Human Cd59 ◽  
Anthrolysin O

<p>Cholesterol-dependent cytolysins (CDCs) are proteinaceous toxins secreted as monomers by some Gram-positive and Gram-negative bacteria that contribute to their pathogenicity. These toxins bind to either cholesterol or human CD59, leading to massive structural changes, toxin oligomerization, formation of very large pores, and ultimately cell death, making these proteins promising targets for inhibition. Myricetin, and its related flavonoids, have been previously identified as a candidate small molecule inhibitor of specific CDCs such as listeriolysin O (LLO) and suilysin (SLY), interfering with their oligomerization. In this work, molecular docking was performed to assess the interaction of myricetin with other CDCs whose crystal structures are already known. Results indicated that although myricetin bound to the hitherto identified cavity in domain 4 (D4), much more efficient and stable binding was obtained in sites along the interfacial regions of domains 1 – 3 (D1 – D3). This was common among the tested CDCs, which was primarily due to much more extensive stabilizing intermolecular interactions, as indicated by post-docking analysis. Specifically, myricetin bound to (1) the interface of the three domains in anthrolysin O (ALO), perfringolysin O (PFO), pneumolysin (PLY), SLY, and vaginolysin (VLY), (2) at/near the D1/D3 interface in LLO and streptolysin O (SLO), and (3) along the D2/D3 interface in intermedilysin (ILY). These findings provide theoretical basis on the possibility of using myricetin and its related compounds as a broad-spectrum inhibitor of CDCs to potentially address the diseases associated with these pathogens.</p>

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